Figure 1. Distribution of mean absolute nucleotide divergence for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)
## Shapiro-Wilk test p-value = 0.519
Figure 2. qqplot for mean dXY distribution for introgression tracts at the 90% threshold
## Shapiro-Wilk test p-value = 0.304
Figure 3. qqplot for mean dXY distribution for species tree tracts at the 90% threshold
## Shapiro-Wilk test p-value = 0.274
Figure 4. qqplot for mean dXY distribution for introgression tracts at the 80% threshold
## Shapiro-Wilk test p-value = 0.58
Figure 5. qqplot for mean dXY distribution for species tree tracts at the 80% threshold
| Tract Type | Posterior Probability | Standard Deviation | Variance |
|---|---|---|---|
| introgression_tract | probability_90 | 0.00138137 | 0.00000191 |
| species_tree_tract | probability_90 | 0.00160160 | 0.00000257 |
| introgression_tract | probability_80 | 0.00064030 | 0.00000041 |
| species_tree_tract | probability_80 | 0.00065455 | 0.00000043 |
| Posterior Probability | Variance Ratio | p | Confidence Interval |
|---|---|---|---|
| 90% | 0.744 | 0.000 | [0.657, 0.842] |
| 80% | 0.957 | 0.487 | [0.845, 1.083] |
| log(90%) | 1.101 | 0.129 | [0.972, 1.246] |
| log(80%) | 1.319 | 0.000 | [1.165, 1.493] |
| Posterior Probability | t | df | p | Confidence Interval |
|---|---|---|---|---|
| 90% | -131.454 | 1955.819 | 0 | [-0.0089, -0.0087] |
| 80% | -258.742 | 1998.000 | 0 | [-0.0075, -0.0074] |
Figure 6. Distribution of mean absolute nucleotide divergence for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)
Figure 7. Distribution of the number of overlapping protein-coding genes per Mb for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)
Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold
Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold
Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold
Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold
| Tract Type | Posterior Probability | Fit | aic |
|---|---|---|---|
| Introgression | 90% | Normal | 3533.1 |
| Introgression | 90% | Log Normal | 3546.5 |
| Introgression | 80% | Normal | 2078.2 |
| Introgression | 80% | Log Normal | 2079.2 |
| Species Tree | 90% | Normal | 4702.2 |
| Species Tree | 90% | Log Normal | 4698.8 |
| Species Tree | 80% | Normal | 4702.2 |
| Species Tree | 80% | Log Normal | 4698.8 |
| Tract Type | Posterior Probability | Standard Deviation | Variance |
|---|---|---|---|
| Introgression | 90% | 1.4135504 | 1.998125 |
| Species Tree | 90% | 2.5362019 | 6.432320 |
| Introgression | 80% | 0.6829458 | 0.466415 |
| Species Tree | 80% | 1.0332989 | 1.067707 |
| Posterior Probability | Variance Ratio | p | Confidence Interval |
|---|---|---|---|
| 90% | 0.311 | 0.000 | [0.274, 0.352] |
| 80% | 0.437 | 0.000 | [0.386, 0.495] |
| log(90%) | 0.839 | 0.006 | [0.741, 0.950] |
| log(80%) | 0.795 | 0.000 | [0.702, 0.900] |
| Posterior Probability | t | df | p | Confidence Interval |
|---|---|---|---|---|
| 90% | -121.046 | 1565.035 | 0 | [-11.2942, -10.934] |
| 80% | -191.011 | 1998.000 | 0 | [-7.5583, -7.4047] |
Figure 10. Distribution of gene counts for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)
Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold
Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold
Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold
Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold
| Tract Type | Posterior Probability | Standard Deviation | Variance |
|---|---|---|---|
| Introgression | 90% | 0.3463958 | 0.11999004 |
| Species Tree | 90% | 0.4826987 | 0.23299805 |
| Introgression | 80% | 0.2368049 | 0.05607657 |
| Species Tree | 80% | 0.1938070 | 0.03756116 |
| Posterior Probability | Variance Ratio | p | Confidence Interval |
|---|---|---|---|
| 90% | 0.515 | 0.000 | [0.455, 0.583] |
| 80% | 1.493 | 0.000 | [1.319, 1.690] |
| log(90%) | 0.999 | 0.989 | [0.883, 1.131] |
| log(80%) | 1.784 | 0.000 | [1.576, 2.019] |
Figure X. Percentage of coding bases for introgression tracts greater than 10 kb in length and the genome-wide background.
Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold
Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold
Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold
Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold
| Tract Type | Posterior Probability | Standard Deviation | Variance |
|---|---|---|---|
| Introgression | 90% | 0.24296527 | 0.05903212 |
| Species Tree | 90% | 0.62125698 | 0.38596023 |
| Introgression | 80% | 0.08270583 | 0.00684025 |
| Species Tree | 80% | 0.25133135 | 0.06316745 |
| Posterior Probability | Variance Ratio | p | Confidence Interval |
|---|---|---|---|
| 90% | 0.153 | 0.000 | [0.135, 0.173] |
| 80% | 0.108 | 0.000 | [0.096, 0.123] |
| log(90%) | 0.818 | 0.002 | [0.723, 0.927] |
| log(80%) | 1.420 | 0.000 | [1.254, 1.608] |
| Posterior Probability | t | df | p | Confidence Interval |
|---|---|---|---|---|
| 90% | -44.111 | 1297.606 | 0 | [-0.9719, -0.8891] |
| 80% | -133.810 | 1998.000 | 0 | [-1.136, -1.1032] |
| Posterior Probability | t | df | p | Confidence Interval |
|---|---|---|---|---|
| 90% | -65.184 | 1078.181 | 0 | [-0.1386, -0.1305] |
| 80% | -34.513 | 1998.000 | 0 | [-0.0456, -0.0407] |
Figure X. mean H. pulcherrimus - S. fragilis dN, dS, and dN/dS for introgression tracts greater than 10 kb in length and the genome-wide background.